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The Phylogenetic Handbook is a broad, hands on guide to theory and practice of nucleotide and protein phylogenetic analysis. This second edition includes six new chapters, covering topics such as Bayesian inference, tree topology testing and the impact of recombination on phylogenies, as well as a detailed section on molecular adaptation. The book has a stronger focus on hypothesis testing than the previous edition, with more extensive discussions on recombination analysis, detecting molecular adaptation and genealogy-based population genetics. Many chapters include elaborate practical sections, which have been updated to introduce the reader to the most recent versions of sequence analysis and phylogeny software, including BLAST, FastA, Clustal, T-coffee, Muscle, DAMBE, Tree-puzzle, Phylip, MEGA, PAUP*, IQPNNI, CONSEL, ModelTest, Prottest, PAML, HYPHY, MrBayes, BEAST, LAMARC, SplitsTree, and RDP. Many analysis tools are described by their original authors, resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate and graduate students.

Evolution. Phylogeny --- Sequence Analysis, DNA --- Sequence Analysis, Protein --- Phylogenèse --- Models, Genetic. --- DNA phylogeny --- Amino Acid Sequence. --- -Proteins --- fylogenetica --- dna analyse --- 575.852 --- 575.852 Biomacromolecules. Molecular evolution --- Biomacromolecules. Molecular evolution --- Branching processes --- Amino Acid Sequences --- Sequence, Amino Acid --- Sequences, Amino Acid --- Protein Structure, Primary --- Primary Protein Structure --- Primary Protein Structures --- Protein Structures, Primary --- Structure, Primary Protein --- Structures, Primary Protein --- Phylogenies --- Models, genetic. --- Sequence analysis, dna --- Sequence analysis, protein --- Phylogenèse --- Phylogeny --- methods --- Computer programs. --- Amino acid sequence --- Cladistic analysis --- DNA --- Proteins --- Models, Genetic --- aminozuur --- dna --- proteine --- Academic collection --- 577.112 --- 577.212.3 --- 577.212.3 Nucleic acid base and sequence compositon. Experimental deciphering of genetic code. --- Nucleic acid base and sequence compositon. Experimental deciphering of genetic code. --- Classification --- Phylogeography --- Proteids --- Biomolecules --- Polypeptides --- Proteomics --- Deoxyribonucleic acid --- Desoxyribonucleic acid --- Thymonucleic acid --- TNA (Nucleic acid) --- Deoxyribose --- Nucleic acids --- Genes --- Cladism --- Cladistic method --- Cladistic taxonomy --- Cladistics --- Cladograms --- Phylogenetic systematics --- Phylogenetic taxonomy --- Taxonomy, Cladistic --- Taxonomy, Phylogenetic --- Biology --- Amino acid sequence analysis --- Analysis, Amino acid sequence --- Peptide sequence --- Peptide sequencing --- Protein sequence --- Protein sequencing --- Sequence, Amino acid --- Amino acids --- Sequence alignment (Bioinformatics) --- Genetic Models --- Genetic Model --- Model, Genetic --- 577.112 Proteins --- Data processing --- Analysis --- Nucleic acid base and sequence compositon. Experimental deciphering of genetic code --- Phylogenomics --- Phylogenomic --- Dna --- Phylogeny. --- Data processing. --- Methods. --- methods. --- Community Phylogenetics --- Molecular Phylogenetics --- Phylogenetic Analyses --- Phylogenetic Analysis --- Phylogenetic Clustering --- Phylogenetic Comparative Analysis --- Phylogenetic Comparative Methods --- Phylogenetic Distance --- Phylogenetic Generalized Least Squares --- Phylogenetic Groups --- Phylogenetic Incongruence --- Phylogenetic Inference --- Phylogenetic Networks --- Phylogenetic Reconstruction --- Phylogenetic Relatedness --- Phylogenetic Relationships --- Phylogenetic Signal --- Phylogenetic Structure --- Phylogenetic Tree --- Phylogenetic Trees --- Analyse, Phylogenetic --- Analysis, Phylogenetic --- Analysis, Phylogenetic Comparative --- Clustering, Phylogenetic --- Community Phylogenetic --- Comparative Analysis, Phylogenetic --- Comparative Method, Phylogenetic --- Distance, Phylogenetic --- Group, Phylogenetic --- Incongruence, Phylogenetic --- Inference, Phylogenetic --- Method, Phylogenetic Comparative --- Molecular Phylogenetic --- Network, Phylogenetic --- Phylogenetic Analyse --- Phylogenetic Clusterings --- Phylogenetic Comparative Analyses --- Phylogenetic Comparative Method --- Phylogenetic Distances --- Phylogenetic Group --- Phylogenetic Incongruences --- Phylogenetic Inferences --- Phylogenetic Network --- Phylogenetic Reconstructions --- Phylogenetic Relatednesses --- Phylogenetic Relationship --- Phylogenetic Signals --- Phylogenetic Structures --- Phylogenetic, Community --- Phylogenetic, Molecular --- Reconstruction, Phylogenetic --- Relatedness, Phylogenetic --- Relationship, Phylogenetic --- Signal, Phylogenetic --- Structure, Phylogenetic --- Tree, Phylogenetic --- Molecular evolution --- Nucleotides --- Nucleotide sequence --- Molecular aspects --- DNA - Analysis - Handbooks, manuals, etc --- Proteins - Analysis - Handbooks, manuals, etc --- Cladistic analysis - Handbooks, manuals, etc --- Amino acid sequence - Data processing